Bio/Search/HSP/HSPI.pm

   1 #-----------------------------------------------------------------
   2 #
   3 # BioPerl module for Bio::Search::HSP::HSPI
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Steve Chervitz <sac@bioperl.org>
   8 # and Jason Stajich <jason@bioperl.org>
   9 #
  10 # You may distribute this module under the same terms as perl itself
  11 #-----------------------------------------------------------------
  12
  13 # POD documentation - main docs before the code
  14
  15 =head1 NAME
  16
  17 Bio::Search::HSP::HSPI - Interface for a High Scoring Pair in a similarity search result
  18
  19 =head1 SYNOPSIS
  20
  21     # Bio::Search::HSP::HSPI objects cannot be instantiated since this
  22     # module defines a pure interface.
  23
  24     # Given an object that implements the Bio::Search::HSP::HSPI  interface,
  25     # you can do the following things with it:
  26
  27     $r_type = $hsp->algorithm;
  28
  29     $pvalue = $hsp->pvalue();
  30
  31     $evalue = $hsp->evalue();
  32
  33     $frac_id = $hsp->frac_identical( ['query'|'hit'|'total'] );
  34
  35     $frac_cons = $hsp->frac_conserved( ['query'|'hit'|'total'] );
  36
  37     $gaps = $hsp->gaps( ['query'|'hit'|'total'] );
  38
  39     $qseq = $hsp->query_string;
  40
  41     $hseq = $hsp->hit_string;
  42
  43     $homology_string = $hsp->homology_string;
  44
  45     $len = $hsp->length( ['query'|'hit'|'total'] );
  46
  47     $rank = $hsp->rank;
  48
  49 =head1 DESCRIPTION
  50
  51 Bio::Search::HSP::HSPI objects cannot be instantiated since this
  52 module defines a pure interface.
  53
  54 Given an object that implements the L<Bio::Search::HSP::HSPI> interface,
  55 you can do the following things with it:
  56
  57 =head1 SEE ALSO
  58
  59 This interface inherits methods from these other modules:
  60
  61 L<Bio::SeqFeatureI>,
  62 L<Bio::SeqFeature::FeaturePair>
  63 L<Bio::SeqFeature::SimilarityPair>
  64
  65 Please refer to these modules for documentation of the
  66 many additional inherited methods.
  67
  68 =head1 FEEDBACK
  69
  70 =head2 Mailing Lists
  71
  72 User feedback is an integral part of the evolution of this and other
  73 Bioperl modules. Send your comments and suggestions preferably to
  74 the Bioperl mailing list.  Your participation is much appreciated.
  75
  76   bioperl-l@bioperl.org                  - General discussion
  77   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  78
  79 =head2 Support
  80
  81 Please direct usage questions or support issues to the mailing list:
  82
  83 I<bioperl-l@bioperl.org>
  84
  85 rather than to the module maintainer directly. Many experienced and
  86 reponsive experts will be able look at the problem and quickly
  87 address it. Please include a thorough description of the problem
  88 with code and data examples if at all possible.
  89
  90 =head2 Reporting Bugs
  91
  92 Report bugs to the Bioperl bug tracking system to help us keep track
  93 of the bugs and their resolution. Bug reports can be submitted via the
  94 web:
  95
  96   https://github.com/bioperl/bioperl-live/issues
  97
  98 =head1 AUTHOR - Steve Chervitz, Jason Stajich
  99
 100 Email sac-at-bioperl.org
 101 Email jason-at-bioperl.org
 102
 103 =head1 COPYRIGHT
 104
 105 Copyright (c) 2001 Steve Chervitz, Jason Stajich. All Rights Reserved.
 106
 107 =head1 DISCLAIMER
 108
 109 This software is provided "as is" without warranty of any kind.
 110
 111 =head1 APPENDIX
 112
 113 The rest of the documentation details each of the object methods.
 114 Internal methods are usually preceded with a _
 115
 116 =cut
 117
 118
 119 # Let the code begin...
 120
 121
 122 package Bio::Search::HSP::HSPI;
 123
 124
 125 use strict;
 126 use Carp;
 127
 128 use base qw(Bio::SeqFeature::SimilarityPair Bio::Root::RootI);
 129
 130
 131 =head2 algorithm
 132
 133  Title   : algorithm
 134  Usage   : my $r_type = $hsp->algorithm
 135  Function: Obtain the name of the algorithm used to obtain the HSP
 136  Returns : string (e.g., BLASTP)
 137  Args    : none
 138
 139 =cut
 140
 141 sub algorithm{
 142    my ($self,@args) = @_;
 143    $self->throw_not_implemented;
 144 }
 145
 146 =head2 pvalue
 147
 148  Title   : pvalue
 149  Usage   : my $pvalue = $hsp->pvalue();
 150  Function: Returns the P-value for this HSP or undef
 151  Returns : float or exponential (2e-10)
 152            P-value is not defined with NCBI Blast2 reports.
 153  Args    : none
 154
 155 =cut
 156
 157 sub pvalue {
 158    my ($self) = @_;
 159    $self->throw_not_implemented;
 160 }
 161
 162 =head2 evalue
 163
 164  Title   : evalue
 165  Usage   : my $evalue = $hsp->evalue();
 166  Function: Returns the e-value for this HSP
 167  Returns : float or exponential (2e-10)
 168  Args    : none
 169
 170 =cut
 171
 172 sub evalue {
 173    my ($self) = @_;
 174    $self->throw_not_implemented;
 175 }
 176
 177
 178 =head2 frac_identical
 179
 180  Title   : frac_identical
 181  Usage   : my $frac_id = $hsp->frac_identical( ['query'|'hit'|'total'] );
 182  Function: Returns the fraction of identitical positions for this HSP
 183  Returns : Float in range 0.0 -> 1.0
 184  Args    : 'query' = num identical / length of query seq (without gaps)
 185            'hit'   = num identical / length of hit seq (without gaps)
 186            'total' = num identical / length of alignment (with gaps)
 187            default = 'total'
 188
 189 =cut
 190
 191 sub frac_identical {
 192    my ($self, $type) = @_;
 193    $self->throw_not_implemented;
 194 }
 195
 196 =head2 frac_conserved
 197
 198  Title    : frac_conserved
 199  Usage    : my $frac_cons = $hsp->frac_conserved( ['query'|'hit'|'total'] );
 200  Function : Returns the fraction of conserved positions for this HSP.
 201             This is the fraction of symbols in the alignment with a
 202             positive score.
 203  Returns : Float in range 0.0 -> 1.0
 204  Args    : 'query' = num conserved / length of query seq (without gaps)
 205            'hit'   = num conserved / length of hit seq (without gaps)
 206            'total' = num conserved / length of alignment (with gaps)
 207            default = 'total'
 208
 209 =cut
 210
 211 sub frac_conserved {
 212     my ($self, $type) = @_;
 213     $self->throw_not_implemented;
 214 }
 215
 216 =head2 num_identical
 217
 218  Title   : num_identical
 219  Usage   : $obj->num_identical($newval)
 220  Function: returns the number of identical residues in the alignment
 221  Returns : integer
 222  Args    : integer (optional)
 223
 224
 225 =cut
 226
 227 sub num_identical{
 228     shift->throw_not_implemented;
 229 }
 230
 231 =head2 num_conserved
 232
 233  Title   : num_conserved
 234  Usage   : $obj->num_conserved($newval)
 235  Function: returns the number of conserved residues in the alignment
 236  Returns : inetger
 237  Args    : integer (optional)
 238
 239
 240 =cut
 241
 242 sub num_conserved{
 243     shift->throw_not_implemented();
 244 }
 245
 246 =head2 gaps
 247
 248  Title    : gaps
 249  Usage    : my $gaps = $hsp->gaps( ['query'|'hit'|'total'] );
 250  Function : Get the number of gap characters in the query, hit, or total alignment.
 251  Returns  : Integer, number of gap characters or 0 if none
 252  Args     : 'query' = num conserved / length of query seq (without gaps)
 253             'hit'   = num conserved / length of hit seq (without gaps)
 254             'total' = num conserved / length of alignment (with gaps)
 255             default = 'total'
 256
 257 =cut
 258
 259 sub gaps        {
 260     my ($self, $type) = @_;
 261     $self->throw_not_implemented;
 262 }
 263
 264 =head2 query_string
 265
 266  Title   : query_string
 267  Usage   : my $qseq = $hsp->query_string;
 268  Function: Retrieves the query sequence of this HSP as a string
 269  Returns : string
 270  Args    : none
 271
 272
 273 =cut
 274
 275 sub query_string{
 276    my ($self) = @_;
 277    $self->throw_not_implemented;
 278 }
 279
 280 =head2 hit_string
 281
 282  Title   : hit_string
 283  Usage   : my $hseq = $hsp->hit_string;
 284  Function: Retrieves the hit sequence of this HSP as a string
 285  Returns : string
 286  Args    : none
 287
 288
 289 =cut
 290
 291 sub hit_string{
 292    my ($self) = @_;
 293    $self->throw_not_implemented;
 294 }
 295
 296 =head2 homology_string
 297
 298  Title   : homology_string
 299  Usage   : my $homo_string = $hsp->homology_string;
 300  Function: Retrieves the homology sequence for this HSP as a string.
 301          : The homology sequence is the string of symbols in between the
 302          : query and hit sequences in the alignment indicating the degree
 303          : of conservation (e.g., identical, similar, not similar).
 304  Returns : string
 305  Args    : none
 306
 307 =cut
 308
 309 sub homology_string{
 310    my ($self) = @_;
 311    $self->throw_not_implemented;
 312 }
 313
 314 =head2 length
 315
 316  Title    : length
 317  Usage    : my $len = $hsp->length( ['query'|'hit'|'total'] );
 318  Function : Returns the length of the query or hit in the alignment (without gaps)
 319             or the aggregate length of the HSP (including gaps;
 320             this may be greater than either hit or query )
 321  Returns  : integer
 322  Args     : 'query' = length of query seq (without gaps)
 323             'hit'   = length of hit seq (without gaps)
 324             'total' = length of alignment (with gaps)
 325             default = 'total'
 326  Args    : none
 327
 328 =cut
 329
 330 sub length{
 331     shift->throw_not_implemented();
 332 }
 333
 334 =head2 percent_identity
 335
 336  Title   : percent_identity
 337  Usage   : my $percentid = $hsp->percent_identity()
 338  Function: Returns the calculated percent identity for an HSP
 339  Returns : floating point between 0 and 100
 340  Args    : none
 341
 342
 343 =cut
 344
 345 sub percent_identity{
 346    my ($self) = @_;
 347    return $self->frac_identical('hsp') * 100;
 348 }
 349
 350 =head2 get_aln
 351
 352  Title   : get_aln
 353  Usage   : my $aln = $hsp->get_aln
 354  Function: Returns a Bio::SimpleAlign representing the HSP alignment
 355  Returns : Bio::SimpleAlign
 356  Args    : none
 357
 358 =cut
 359
 360 sub get_aln {
 361    my ($self) = @_;
 362    $self->throw_not_implemented;
 363 }
 364
 365
 366 =head2 seq_inds
 367
 368  Title   : seq_inds
 369  Purpose   : Get a list of residue positions (indices) for all identical
 370            : or conserved residues in the query or sbjct sequence.
 371  Example   : @s_ind = $hsp->seq_inds('query', 'identical');
 372            : @h_ind = $hsp->seq_inds('hit', 'conserved');
 373            : @h_ind = $hsp->seq_inds('hit', 'conserved', 1);
 374  Returns   : List of integers
 375            : May include ranges if collapse is true.
 376  Argument  : seq_type  = 'query' or 'hit' or 'sbjct'  (default = query)
 377               ('sbjct' is synonymous with 'hit')
 378              class     = 'identical' or 'conserved' or 'nomatch' or 'gap'
 379                           (default = identical)
 380                           (can be shortened to 'id' or 'cons')
 381
 382              collapse  = boolean, if true, consecutive positions are merged
 383                          using a range notation, e.g., "1 2 3 4 5 7 9 10 11"
 384                          collapses to "1-5 7 9-11". This is useful for
 385                          consolidating long lists. Default = no collapse.
 386  Throws    : n/a.
 387  Comments  :
 388
 389 See Also   : L<Bio::Search::BlastUtils::collapse_nums()|Bio::Search::BlastUtils>, L<Bio::Search::Hit::HitI::seq_inds()|Bio::Search::Hit::HitI>
 390
 391 =cut
 392
 393 sub seq_inds {
 394     shift->throw_not_implemented();
 395 }
 396
 397 =head2 Inherited from L<Bio::SeqFeature::SimilarityPair>
 398
 399 These methods come from L<Bio::SeqFeature::SimilarityPair>
 400
 401 =head2 query
 402
 403  Title   : query
 404  Usage   : my $query = $hsp->query
 405  Function: Returns a SeqFeature representing the query in the HSP
 406  Returns : Bio::SeqFeature::Similarity
 407  Args    : [optional] new value to set
 408
 409
 410 =head2 hit
 411
 412  Title   : hit
 413  Usage   : my $hit = $hsp->hit
 414  Function: Returns a SeqFeature representing the hit in the HSP
 415  Returns : Bio::SeqFeature::Similarity
 416  Args    : [optional] new value to set
 417
 418
 419 =head2 significance
 420
 421  Title   : significance
 422  Usage   : $evalue = $obj->significance();
 423            $obj->significance($evalue);
 424  Function: Get/Set the significance value (see Bio::SeqFeature::SimilarityPair)
 425  Returns : significance value (scientific notation string)
 426  Args    : significance value (sci notation string)
 427
 428
 429 =head2 score
 430
 431  Title   : score
 432  Usage   : my $score = $hsp->score();
 433  Function: Returns the score for this HSP or undef
 434  Returns : numeric
 435  Args    : [optional] numeric to set value
 436
 437 =head2 bits
 438
 439  Title   : bits
 440  Usage   : my $bits = $hsp->bits();
 441  Function: Returns the bit value for this HSP or undef
 442  Returns : numeric
 443  Args    : none
 444
 445 =cut
 446
 447 # override
 448
 449 =head2 strand
 450
 451  Title   : strand
 452  Usage   : $hsp->strand('query')
 453  Function: Retrieves the strand for the HSP component requested
 454  Returns : +1 or -1 (0 if unknown)
 455  Args    : 'hit' or 'subject' or 'sbjct' to retrieve the strand of the subject
 456            'query' to retrieve the query strand (default)
 457            'list' or 'array' to retrieve both query and hit together
 458
 459 =cut
 460
 461 sub strand {
 462     my $self = shift;
 463     my $val  = shift;
 464     $val = 'query' unless defined $val;
 465     $val =~ s/^\s+//;
 466
 467     if ( $val =~ /^q/i ) {
 468         return $self->query->strand(@_);
 469     }
 470     elsif ( $val =~ /^hi|^s/i ) {
 471         return $self->hit->strand(@_);
 472     }
 473     elsif ( $val =~ /^list|array/i ) {
 474
 475         # Do we really need to pass on additional arguments here? HL
 476         # (formerly this was strand(shift) which is really bad coding because
 477         # it breaks if the callee allows setting to undef)
 478         return ( $self->query->strand(@_), $self->hit->strand(@_) );
 479     }
 480     else {
 481         $self->warn("unrecognized component '$val' requested\n");
 482     }
 483     return 0;
 484 }
 485
 486 =head2 start
 487
 488  Title   : start
 489  Usage   : $hsp->start('query')
 490  Function: Retrieves the start for the HSP component requested
 491  Returns : integer
 492  Args    : 'hit' or 'subject' or 'sbjct' to retrieve the start of the subject
 493            'query' to retrieve the query start (default)
 494
 495 =cut
 496
 497 sub start {
 498     my $self = shift;
 499     my $val = shift;
 500     $val = 'query' unless defined $val;
 501     $val =~ s/^\s+//;
 502
 503     if( $val =~ /^q/i ) {
 504         return $self->query->start(@_);
 505     } elsif( $val =~ /^(hi|s)/i ) {
 506         return $self->hit->start(@_);
 507     } elsif (  $val =~ /^list|array/i ) {
 508         # do we really need to pass on additional arguments here? HL
 509         # (formerly this was strand(shift) which is really bad coding because
 510         # it breaks if the callee allows setting to undef)
 511         return ($self->query->start(@_),
 512                 $self->hit->start(@_) );
 513     } else {
 514         $self->warn("unrecognized component '$val' requested\n");
 515     }
 516     return 0;
 517 }
 518
 519 =head2 end
 520
 521  Title   : end
 522  Usage   : $hsp->end('query')
 523  Function: Retrieves the end for the HSP component requested
 524  Returns : integer
 525  Args    : 'hit' or 'subject' or 'sbjct' to retrieve the end of the subject
 526            'query' to retrieve the query end (default)
 527
 528 =cut
 529
 530 sub end {
 531     my $self = shift;
 532     my $val = shift;
 533     $val = 'query' unless defined $val;
 534     $val =~ s/^\s+//;
 535
 536     if( $val =~ /^q/i ) {
 537         return $self->query->end(@_);
 538     } elsif( $val =~ /^(hi|s)/i ) {
 539         return $self->hit->end(@_);
 540     } elsif (  $val =~ /^list|array/i ) {
 541         # do we really need to pass on additional arguments here? HL
 542         # (formerly this was strand(shift) which is really bad coding because
 543         # it breaks if the callee allows setting to undef)
 544         return ($self->query->end(@_),
 545                 $self->hit->end(@_) );
 546     } else {
 547         $self->warn("unrecognized end component '$val' requested\n");
 548     }
 549     return 0;
 550 }
 551
 552 =head2 seq
 553
 554  Usage     : $hsp->seq( [seq_type] );
 555  Purpose   : Get the query or sbjct sequence as a Bio::Seq.pm object.
 556  Example   : $seqObj = $hsp->seq('query');
 557  Returns   : Object reference for a Bio::Seq.pm object.
 558  Argument  : seq_type = 'query' or 'hit' or 'sbjct' (default = 'query').
 559            :  ('sbjct' is synonymous with 'hit')
 560            : default is 'query'
 561  Throws    : Propagates any exception that occurs during construction
 562            : of the Bio::Seq.pm object.
 563  Comments  : The sequence is returned in an array of strings corresponding
 564            : to the strings in the original format of the Blast alignment.
 565            : (i.e., same spacing).
 566
 567 See Also   : L</seq_str>, L</seq_inds>, L<Bio::Seq>
 568
 569 =cut
 570
 571 sub seq {
 572     my($self,$seqType) = @_;
 573     $seqType ||= 'query';
 574     $seqType = 'sbjct' if $seqType eq 'hit';
 575     my $str = $self->seq_str($seqType);
 576     if( $seqType =~ /^(m|ho)/i ) {
 577         $self->throw("cannot call seq on the homology match string, it isn't really a sequence, use get_aln to convert the HSP to a Bio::AlignIO and generate a consensus from that.");
 578     }
 579     require Bio::LocatableSeq;
 580     my $id = $seqType =~ /^q/i ? $self->query->seq_id : $self->hit->seq_id;
 581     return Bio::LocatableSeq->new(  -ID        => $id,
 582                                     -SEQ       => $str,
 583                                     -START     => $self->start($seqType),
 584                                     -END       => $self->end($seqType),
 585                                     -STRAND    => $self->strand($seqType),
 586                                     -FORCE_NSE => $id ? 0 : 1,
 587                                     -DESC      => "$seqType sequence " );
 588 }
 589
 590 =head2 seq_str
 591
 592  Usage     : $hsp->seq_str( seq_type );
 593  Purpose   : Get the full query, sbjct, or 'match' sequence as a string.
 594            : The 'match' sequence is the string of symbols in between the
 595            : query and sbjct sequences.
 596  Example   : $str = $hsp->seq_str('query');
 597  Returns   : String
 598  Argument  : seq_Type = 'query' or 'hit' or 'sbjct' or 'match'
 599            :  ('sbjct' is synonymous with 'hit')
 600            : default is 'query'
 601  Throws    : Exception if the argument does not match an accepted seq_type.
 602  Comments  :
 603
 604 See Also   : L</seq>, L</seq_inds>, C<_set_match_seq>
 605
 606 =cut
 607
 608 sub seq_str {
 609     my $self = shift;
 610     my $type = shift || 'query';
 611
 612     if( $type =~ /^q/i ) { return $self->query_string(@_) }
 613     elsif( $type =~ /^(s)|(hi)/i ) { return $self->hit_string(@_)}
 614     elsif ( $type =~ /^(ho)|(ma)/i  ) { return $self->homology_string(@_) }
 615     else {
 616         $self->warn("unknown sequence type $type");
 617     }
 618     return '';
 619 }
 620
 621
 622 =head2 rank
 623
 624  Usage     : $hsp->rank( [string] );
 625  Purpose   : Get the rank of the HSP within a given Blast hit.
 626  Example   : $rank = $hsp->rank;
 627  Returns   : Integer (1..n) corresponding to the order in which the HSP
 628              appears in the BLAST report.
 629
 630 =cut
 631
 632 sub rank { shift->throw_not_implemented }
 633
 634 =head2 matches
 635
 636  Usage     : $hsp->matches(-seq   => 'hit'|'query',
 637                            -start => $start,
 638                            -stop  => $stop);
 639  Purpose   : Get the total number of identical and conservative matches
 640            : in the query or sbjct sequence for the given HSP. Optionally can
 641            : report data within a defined interval along the seq.
 642            : (Note: 'conservative' matches are called 'positives' in the
 643            : Blast report.)
 644  Example   : ($id,$cons) = $hsp_object->matches(-seq   => 'hit');
 645            : ($id,$cons) = $hsp_object->matches(-seq   => 'query',
 646                                                 -start => 300,
 647                                                 -stop  => 400);
 648  Returns   : 2-element array of integers
 649  Argument  : (1) seq_type = 'query' or 'hit' or 'sbjct' (default = query)
 650            :  ('sbjct' is synonymous with 'hit')
 651            : (2) start = Starting coordinate (optional)
 652            : (3) stop  = Ending coordinate (optional)
 653  Throws    : Exception if the supplied coordinates are out of range.
 654  Comments  : Relies on seq_str('match') to get the string of alignment symbols
 655            : between the query and sbjct lines which are used for determining
 656            : the number of identical and conservative matches.
 657
 658 See Also   : L</length>, L</gaps>, L</seq_str>, L<Bio::Search::Hit::BlastHit::_adjust_contigs()|Bio::Search::Hit::BlastHit>
 659
 660 =cut
 661
 662 #-----------
 663 sub matches {
 664 #-----------
 665     my( $self, %param ) = @_;
 666     my(@data);
 667     my($seqType, $beg, $end) = ($param{-SEQ},
 668                                 $param{-START},
 669                                 $param{-STOP});
 670     $seqType ||= 'query';
 671     $seqType = 'sbjct' if $seqType eq 'hit';
 672
 673     if( (!defined $beg && !defined $end) || ! $self->seq_str('match') ) {
 674         ## Get data for the whole alignment.
 675         push @data, ($self->num_identical, $self->num_conserved);
 676     } else {
 677
 678         ## Get the substring representing the desired sub-section of aln.
 679         $beg ||= 0;
 680         $end ||= 0;
 681         my($start,$stop) = $self->range($seqType);
 682         if($beg == 0) { $beg = $start; $end = $beg+$end; } # sane?
 683         elsif($end == 0) { $end = $stop; $beg = $end-$beg; } # sane?
 684
 685         if($end > $stop) { $end = $stop; }
 686         if($beg < $start) { $beg = $start; }
 687
 688         # now with gap handling! /maj
 689         my $match_str = $self->seq_str('match');
 690         if ($self->gaps) {
 691             # strip the homology string of gap positions relative
 692             # to the target type
 693             $match_str = $self->seq_str('match');
 694             my $tgt   = $self->seq_str($seqType);
 695             my $encode = $match_str ^ $tgt;
 696             my $zap = '-'^' ';
 697             $encode =~ s/$zap//g;
 698             $tgt =~ s/-//g;
 699             $match_str = $tgt ^ $encode;
 700         }
 701
 702         ## ML: START fix for substr out of range error ------------------
 703         my $seq = "";
 704         if (($self->algorithm =~ /TBLAST[NX]/) && ($seqType eq 'sbjct'))
 705         {
 706             $seq = substr($match_str,
 707                           int(($beg-$start)/3),
 708                           int(($end-$beg+1)/3));
 709
 710         } elsif (($self->algorithm =~ /T?BLASTX/) && ($seqType eq 'query')) {
 711             $seq = substr($match_str,
 712                           int(($beg-$start)/3), int(($end-$beg+1)/3));
 713         } else {
 714             $seq = substr($match_str,
 715                           $beg-$start, ($end-$beg+1));
 716         }
 717         ## ML: End of fix for  substr out of range error -----------------
 718
 719         if(!CORE::length $seq) {
 720             $self->throw("Undefined sub-sequence ($beg,$end). Valid range = $start - $stop");
 721         }
 722
 723         $seq =~ s/ //g;  # remove space (no info).
 724         my $len_cons = CORE::length $seq;
 725         $seq =~ s/\+//g;  # remove '+' characters (conservative substitutions)
 726         my $len_id = CORE::length $seq;
 727         push @data, ($len_id, $len_cons);
 728     }
 729     @data;
 730 }
 731
 732 =head2 n
 733
 734  Usage     : $hsp_obj->n()
 735  Purpose   : Get the N value (num HSPs on which P/Expect is based).
 736            : This value is not defined with NCBI Blast2 with gapping.
 737  Returns   : Integer or null string if not defined.
 738  Argument  : n/a
 739  Throws    : n/a
 740  Comments  : The 'N' value is listed in parenthesis with P/Expect value:
 741            : e.g., P(3) = 1.2e-30  ---> (N = 3).
 742            : Not defined in NCBI Blast2 with gaps.
 743            : This typically is equal to the number of HSPs but not always.
 744            : To obtain the number of HSPs, use Bio::Search::Hit::HitI::num_hsps().
 745
 746 See Also   : L<Bio::SeqFeature::SimilarityPair::score()|Bio::SeqFeature::SimilarityPair>
 747
 748 =cut
 749
 750 sub n { shift->throw_not_implemented }
 751
 752 =head2 range
 753
 754  Usage     : $hsp->range( [seq_type] );
 755  Purpose   : Gets the (start, end) coordinates for the query or sbjct sequence
 756            : in the HSP alignment.
 757  Example   : ($query_beg, $query_end) = $hsp->range('query');
 758            : ($hit_beg, $hit_end) = $hsp->range('hit');
 759  Returns   : Two-element array of integers
 760  Argument  : seq_type = string, 'query' or 'hit' or 'sbjct'  (default = 'query')
 761            :  ('sbjct' is synonymous with 'hit')
 762  Throws    : n/a
 763  Comments  : This is a convenience method for constructions such as
 764              ($hsp->query->start, $hsp->query->end)
 765
 766 =cut
 767
 768 sub range { shift->throw_not_implemented }
 769
 770 sub expect { shift->evalue(@_) }
 771
 772 1;
 773